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Higaki Laboratory

Welcome to the laboratory of Dr. Takumi Higaki at Kumamoto University.
We are interested in cytoskeleton dynamics in plant cell morphogenesis.

We accomplished time-sequential observations of plant actin filaments throughout cell cycle with GFP-tagged actin binding domain 2 of fimbrin that is an actin side-binding protein (Sano and Higaki et al. 2005 Plant J, Higaki et al. 2006 Plant Cell Physiol, Higaki et al. 2007 Plant Cell Physiol, Higaki et al. 2007 Curr Opin Plant Biol, Higaki et al. 2008 BMC Plant Biol). We also developed microscopic image analysis frameworks to quantitatively evaluate bundling, orientation, and density of actin filaments. Live cell imaging and the image processing techniques revealed that actin filaments were transiently bundled prior to stomatal opening, suggesting crucial roles of actin bundling in diurnal cycle-dependent stomatal opening (Higaki et al. 2010 Plant J). Based on the image processing techniques, we performed various collaborative works in plant cell biology field. In particular, we revealed intracellular dynamics in stomatal movements (Higaki et al. 2012 Sci Rep, Higaki et al. 2013 BMC Plant Biol, Hashimoto-Sugimoto and Higaki et al. 2013 Nature Commun, Higaki et al. 2014 Plant Cell Physiol, Higaki 2016 J Vis Exp), auxin response (Takahashi et al. 2016 Plant J), asymmetric cell division of zygotes (Kimata and Higaki et al. 2016 PNAS), plant immunity (Shimono and Higaki et al. 2016 PLOS One, Inada and Higaki et al. 2016 Plant Physiol, Inada and Higaki et al. 2016 J Plant Res), determination of cell division plane (Kojo and Higaki et al. 2013 Plant Cell Physiol), cell wall regeneration during protoplast culture (Yoneda et al. 2010 Plant J) and cytoplasmic streaming in Marchantia polymorpha (Era et al. 2013 J Plant Res). Some of these works appeared on the cover of international journals as shown below.

In addition, we developed CARTA (Clustering-Aided Rapid Training Agent), which is a computer software for rapid and accurate classification of the biomedical images based on active learning with iterative clustering (Kutsuna and Higaki et al. 2012 Nature Commun). Based on the CARTA methods, we also developed the computer-assisted system to detect the structures of interest, such as organelles (Higaki et al. 2015 Sci Rep). Furthermore, we tried to understand roles of microtubules in plant cell morphogenesis by an approach combining quantitative image processing and mathematical modeling. We proposed mathematical models to explain cell morphogenesis with microtubule distributions. The models successfully reproduce pattern formation observed in planta (Higaki et al. 2016 PLOS Comput Biol, Higaki et al. 2017 Plant Cell Physiol).

In plant cell biology field, manual evaluation of cellular structures with microscopic images is still a popular approach. However, the manual approach is laborious and is prone to error, especially when large quantities of microscopic image data need to be analyzed. Therefore, we have great interests in development of microscopic image processing techniques. We have actually been working on development of the image analysis methods that overcome these limitations by quantification of cytoskeletal organizations, as described above. We would like to continue to develop image analysis tools to solve cell biological problems. Of course, in addition to the so-called ‘dry’ works, we will continue to be experimental cell biologists, so-called ‘wet’ researchers. We believe that development and refinement of the practical image analysis techniques and appropriate use of them would allow us to discover new aspects of cytoskeletons.

Research examples in the Higaki laboratory:

1. Actin filaments in plant cells

Actin, a protein that is ubiquitous in eukaryotes, forms actin filaments by its polymerization under physiological conditions. Actin filaments are deeply involved in cell morphological changes through formation of higher-order structures such as networks and bundles. In the case of plant cells, actin filaments regulate various organelle morphology and movements. We aim for visible understanding of actin filament roles in cell division, cell expansion, and cell death, in which plant cell undergoes dynamic morphological changes.

1. Actin filaments in plant cells
2. Stomatal development and movement

The stomata on the plant leaf and stem surfaces is essential for plant survival because they are responsible for gaseous exchange and transpiration. The stomatal density and aperture is appropriately regulated in response to environmental cues. Using multiple approaches including biochemistry, molecular biology, live cell imaging, image analysis, and mathematical modeling, we aim for visible understanding of the multi-scale spatiotemporal control mechanism of plant stomata.

2. Stomatal development and movement
3. Image analysis tool development

When addressing problems in the cell biological studies described above, quantitative evaluations of cell structure and movement involving microscopic image analyses are essential. However, existing image analysis softwares are frequently insufficient. This is because the acquired image types and objectives are highly diversified in cell biology studies. For this reason, we are developing image analysis tools that would promote research progress from the standpoint of experimental cell biologists.

3. Image analysis tool development
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